


The [E]nd becomes a new beginning

by Desphiria



Category: NieR: Automata (Video Game)
Genre: Alternate Ending, Drama, F/M, Gen, Self-Insert
Language: English
Status: Completed
Published: 2018-04-29
Updated: 2018-04-29
Packaged: 2019-04-29 19:03:12
Rating: General Audiences
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 1
Words: 4,752
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/14479167
Author URL: https://archiveofourown.org/users/Desphiria/pseuds/Desphiria
Summary: Disclaimer - I do not own any of the characters from NieR: Automata except for the original characters 56B and 13S. NieR: Automata is owned by Platinum Games and Square Enix.SPOILER ALERT - This story has been mixed with Endings D and E of the game to make this Alternate Ending story. If you haven't finished the game yet then you might not want to read this until you finish.





	The [E]nd becomes a new beginning

**Author's Note:**

> I know the story's pretty long and I wasn't sure if breaking it up into chapters was a good idea, but I really liked it and enjoyed writing it. So, I wanted to share my story with you guys and I hope you all like it too!

“ _Even though fighting isn’t my thing, I’ll do everything in my power to protect you. I promise.”_

 

13S was jolted awake by the sound of the alarm going off throughout the bunker and everything around her shaking. Had she fallen asleep while performing her hacking duties?  
Before she could fully process what was going on, the door to her room had opened and standing in the doorway was her partner, 56B.  
“Get up, we have to go. Now.” He ordered.  
“Wait... why? What’s going-”  
“I don’t have time to explain!” He exclaimed, running towards her and pulling her up by her arm, as a YoRHa member suddenly rushed towards them.  
56B quickly drew his sword and pushed her back, blocking her attacks and striking her when there was an opening.  
“What’s happening? Why are they all-?”  
“Thirteen!” A familiar voice cut through, what sounded like shrieking and childish laughter that was just downright unsettling.  
“Nines? What’s going on? Why is everyone acting so strange?” She asked, looking around as more of the YoRHa members on base began attacking them.  
56B ran over to 2B and stood beside her to help fight off their assailants.  
“Everyone’s been infected with a virus.” A mature, female voice answered from behind them.  
“Did you say a virus?”  
“Thirteen, let me see your eyes.” 9S instructed, gently gripping her face and turning her head towards him.  
13S removed her blindfold-like visor and gazed at him with her black eyes.  
“Do you feel angry or violent?” Nines asked, hints of worry in his voice.  
13S shook her head. “I...feel fine right now.” She responded, replacing her visor.  
“We have to get out of here before the Bunker collapses in on us.” 2B informed, as she stood in front of the group.  
“The fastest way out of here is by flight unit.” 9S responded.  
“Let’s get going.” 2B said, taking the lead and running down the hall as everyone followed close behind her.

 

As the five of them made their way towards the hangar, more YoRHa units emerged from their rooms and attacked them.  
56B and 2B were both in front, defending the two Scanner models and the Commander, with 9S helping them out if one of them managed to bypass the two B Types.  
“Quickly, get to the flight units!” 2B exclaimed, as 9S and 13S entered the room.  
“You too Commander, hurry!” She called.  
“I can’t.” The Commander replied, opening her eyes to reveal that they had completely turned red.  
“Commander...”  
“The… Commander’s infected too?” 13S whispered, turning around to see that her partner was no longer with her.  
Looking around, she spotted him standing beside the Commander, looking away from them.  
“Fifty-six? You’re coming with us too… right?” The female Scanner type asked, gazing at the red haired male.  
“I’m sorry Thirteen, but I’m afraid that… I can’t either.” He responded, glancing at his partner and revealing that he too had become infected.  
13S gasped and stepped back, covering her mouth.  
“You too? But, how?” She asked, sadness evident in her voice.  
“They were both, connected to the server.” 9S responded from behind her.  
“Can’t we fix this somehow?!”  
“If they would allow me to hack into their systems then, maybe...”  
“I’m afraid that there’s no time. You three are the last remaining members of YoRHa and I expect you to take care of each other. Just know that, I enjoyed working with you.” The Commander told them.  
“9S,” 56B called, turning fully towards them.  
“As of now, I entrust the well-being of 13S to you.” He said, a serious expression on his face.  
“Take care of her for me.”  
“Right.” 9S replied, nodding firmly as he reached out and took her hand.  
“No… this isn’t right.” 13S whispered.  
“This shouldn’t be happening. We can’t just leave them here to die. There has to be… **something** we can do.”  
9S turned to her and shook his head. “If there is, we don’t have time for it. We really should get going before the Bunker explodes with us inside.”  
“Goodbye 2B, take care of them for me.” The Commander said.  
“Remember your promise, 9S.” 56B added.  
“13S, you were like a little sister to me and I enjoyed working with you.”  
2B and 9S nodded, quickly making their way over to their flight units and climbing in, taking off as the Bunker began to shake violently, the sound of collapsing walls could be heard from behind the door.

  
“How? How did this... **why** did this happen!?” 13S suddenly exclaimed.  
“Why was every YoRHa member infected with the logic virus at the same time?! How did it progress so quickly?!”  
“We don’t know! We were on the ground, following orders to help the other squads when everyone suddenly began to act strange.”  
“We were fighting machine lifeforms and once we defeated them, we were caught off guard by them having some weird… EMP emitter hidden in their heads.” 2B explained.  
“Then all I remember is this searing pain, before everything went black.”  
“I.. didn’t know what else to do so, I hacked into our systems and severed the tie between us and the server.” 9S explained.  
“But due to us having to use our black boxes to destroy the ones who were attacking us on the ground, we awoke back at the Bunker before the attack.”  
“Do you think it has something to do with Eve?” 13S asked curiously.  
“It couldn’t be. We destroyed him.”  
“So if this has nothing to do with him then, how did the virus get into the server?” She asked.  
“I… may know but...”

Before they could get any further, the word _ALERT_ began to flash across their screens.

“Oh no...”  
“Are they YoRHa units?” 9S asked.

“What should we do? With how many are arriving, we can’t take all of them at once can we?” 13S asked, staring at her screen.

“We don’t have a choice, here they come!” 2B announced.

 

Multiple infected YoRHa units came into view and immediately engaged them, firing shot after shot at them along with missiles and energy balls they had to dodge.  
Attacking and destroying them was a fruitless endeavor, since no matter how many they took out, others would quickly replace them.  
“They just keep coming!” 13S exclaimed, firing shot after shot at the advancing army.  
“9S, I need you to get 13S to safety!” 2B ordered.  
“These units are endless. I’m going to lure them away and I need you both to escape. Split up if you have to, just don’t let them catch you.”  
“What about you? We can’t just let you take them on by yourself!” 9S retorted.  
“Let us help you lure them away, at least!” 13S offered.  
“No! 9S, you have a promise to fulfill and I won’t allow you to break it. Take 13S and get out of here!”  
“2B, we’re not going to just let you face them alone! You could die!”  
“That’s an order 9S! Take 13S and GO! I’ll take care of the infected YoRHa and buy you both some time!”  
“But…!”  
“Nines, we have no choice but to listen to her! If we stay here any longer, we’re either going to hinder her or become surrounded by the enemy!”  
9S was extremely hesitant to leave 2B alone to deal with the enemies by herself but, 13S was right.  
They had no choice but to leave and at this rate, they would most likely be exhausted by the time they finished.  
“Dammit! Don’t die on us 2B!” 9S exclaimed, quickly flying ahead with 13S in tow. Splitting up part way through so they wouldn’t draw attention to each other.

 

Arriving on Earth, 13S landed her flight unit in front of the castle in the Amusement Park.  
“Pod, locate 9S.” She instructed, getting out and looking around, taking in her surroundings.  
The Amusement park had changed. It was quiet now, and there was no music playing whatsoever.  
No smiling machines could be seen walking around and throwing their colored papers. Even the automatic fireworks had stopped working.  
_‘_ _What happened here?’_ She wondered.  
Most of the robots that were seen previously wandering around were gone, leaving only a few of them left.  
“9S has been located and is currently heading in the direction of the abandoned commercial district.”

Quickly 13S made her way in that direction, hoping that by the time she found him, 2B would be there as well.

 

Reaching her destination, 13S couldn’t believe her eyes.  
2B was lying on the ground, bleeding out from a stomach wound.  
“2B! Are you alright?!” She exclaimed, running over and kneeling beside her.  
“Who did this to you?!” She asked, looking around for something that could stop the bleeding as she placed her hand against the wound.  
2B however, remained silent and motionless. Her eyes closed with a peaceful expression on her face.  
“I’m so sorry 2B, if only I had found you sooner… maybe I would have been able to help.” She said, gazing at the android’s lifeless body.  
“I don’t think Nines is here. Pod, can you find out where he went?”

“9S is currently heading towards the City Ruins where the tower was seen emerging from the ground.”  
“Tower?” 13S asked as she turned around, her eyes widening as she got a glimpse of the white spires protruding from the ground, laying against a large ivory tower that looked like a rocket ship.  
How did she not notice that when she landed?  
With a determined look upon her face, the female Scanner type sprinted towards the City Ruins.

 

What she saw once she arrived was fascinating. There were four small ivory pillars protruding from the ground and the tower itself housed a rather large door in the middle of it.  
In the distance leaning against the building, 9S could make out what looked like two bodies.  
“What… the hell?” She wondered, gliding down and running over to them.  
“Hey, are you two alright?!” She called, inspecting them once she got close enough.  
The two bodies looked the same, save for their hairstyles.  
One was leaning against the other, as they both leaned against the wall barely moving.  
“Hey, can you hear me?”  
“Did...we help?” The one with a mature voice and long wavy hair, asked weakly.  
“Help? Help with what exactly?” 13S asked, examining them closely.  
“Were...were we able to atone for our sins?”  
“What sins are you talking about?”  
“We made up for them by helping 9S get into the tower… right?” The female android asked, looking up at her.

“Nines went in there?” She asked, turning her dark gaze upon the door.  
The woman didn’t respond. Thirteen wanted so badly to investigate what caused this.  
What was it that hurt them this badly?  
What did the conscious one mean by, ‘atone for our sins’?  
Better yet, what ‘sins’ were they trying to atone for?  
“I’m sure that… whatever sins you committed, the gods have forgiven you.” She reassured.  
“So, I would say that yes...you atoned.” She told the woman, not even sure if she could hear her anymore, before standing up and making her way inside the mysterious building.

 

The further in she got, the more carnage she could see. 13S entered a darkened room, where she noticed that there were many android bodies that looked familiar, lying on the ground.  
“What… happened here? Where did all these bodies come from and why do they look like 2B?”  
“Scanners indicate that 9S has been through here and that these bodies are the result of an attack. I will assume that the reason they all look like 2B, is to speed up the progress of android 9S’s condition.”  
“Condition? What’s wrong with 9S?” She asked.  
“I have been informed by Pod 153 that 9S has been suffering from the Logic Virus, and that his mental state has been steadily deteriorating.”  
“That makes no sense. He disconnected from the server, how did he get infected too?” She asked, her voice full of concern and confusion.  
“It has been determined that the activation of the virus was caused by the murder of 2B that 9S witnessed.” Pod 428 explained.  
“Has his pod tried to get him treated?”  
“Affirmative. However android 9S has refused any and all kinds of help that was suggested by Pod 153.”  
The room had gone silent until 13S asked, “Is there a way for him to be cured if found?”  
“Uncertain. There may be a possibility but, it could be dangerous to attempt if the subject has become completely corrupted.”  
“We’ll have to try, but first we have to find him.” She said, taking a deep breath and making her way through the rest of the tower.

 

Deep within the tower, 13S came upon a room made of nothing but white blocks and empty space.  
There were a few bodies there as well but not as many as there were in the room before.  
_‘Just hold on for a little longer Nines, I’ll be there soon and then we can get out of here together.’_ She thought, eventually coming upon an empty room with an open hallway.

  
“It appears that, we have another guest.” Came the sound of two voices, that seemed to be mimicking that of a little girl yet mixing with the voice of an older male.  
Turning towards the sound, there before her were holographic images of little girls who were both wearing red and looked exactly the same.  
“Where is 9S?!” She asked, glaring at them.

The girls stared at her for a while before answering, “9S is being taken care of as we speak.”  
“What do you mean, by ‘taken care of’? What have you done to him?!”  
“We have done nothing that he hasn’t already done to himself.”  
“What does that even mean?!”

“What would anyone seeking revenge do, when facing down their opponent?”

13S stared at them, pondering the question. Her eyes widening when the realization hit home, he was fighting with intent to kill.

“Where is he?! Is he down the hall?!” She asked, trying to think of a way to get around them.  
“Perhaps, but you may not like what you see.” They answered, moving from in front of the open doorway.  
“You will probably lose him to her if you’re not fast enough.” They added.  
Were they just going to let her through without a fight?  
13S quickly bolted down the corridor, her mind racing. What did those girls mean by losing him to her?  
She was sure they had meant A2 but, did that mean she was stronger than 9S?  
She realized that made sense. Even though he and a few other scanners were probably capable of some combat techniques, 9S wasn’t much of a fighter and she knew this.  
However, when facing someone stronger…  
No, being a Scanner type meant their hacking skills were good enough to kill, since they were able to detonate or control the enemy they hacked.  
If 9S was constantly hacking A2, wouldn’t that be enough for him to win?  
Was his hacking really strong enough to take down someone like that alone?  
Wait...didn’t her Pod say that Nines was suffering from the Logic Virus and he had been refusing to recover his system?  
If that was the case then…  


“Nines!” 13S cried out as she entered the room, managing to grab 9S’s attention.  
The look in his eyes was evidence enough that he had been completely corrupted.  
“Nines, you don’t have to do this! Let’s just go home and forget all about what happened!” She exclaimed.

“Home? Have you forgotten that we don’t have a home anymore, Thirteen? The Bunker has been destroyed, and the YoRHa are no longer needed on this planet. There’s nowhere for us to go now.” He informed her, his voice sounding deranged.  
“We can always make a new home **here!** We could join the resistance or just live a normal life like we always dreamed of, just the two of us!”  
“Not without 2B, right 9S?” A2 interrupted, her light blue gaze locked onto the male in front of her.  
“It won’t be the same without her, right? Even if she hated killing you.”  
9S didn’t answer, his manic gaze locked onto the rebel android standing in front of him.

A deep frown appeared on the young android’s face. Did 2B really mean more to 9S than she did?  
“I… I know it won’t be the same but, what about your promise to Fifty-six? What about the promise you made to me? Aren’t I enough for you?” She asked, her voice cracking as her eyes began to well with tears.  
Yet, 9S didn’t respond.  
“Nines answer me! Don’t I mean more to you than 2B did?! Don’t you remember all the time we spent together and how many times you told me that you cared for me?! That you would do everything in your power to protect me, even though fighting wasn’t your thing?! Have you really forgotten all of those times?!” She exclaimed, her black eyes lingering on him.  
“ **Answer me!** ”  
“You won’t be able to get through to him in his current mental state.” A2 said, pointing her sword at him.  
“So I suggest you stay back while I take care of this, and hope that I don’t kill him.” A2 said, jumping back then quickly charging at 9S with her blade drawn, rushing forward and striking at him again and again, dodging and blocking a few of his attacks but being unable to dodge the hacking attempts he used when there was an opening, along with his Pod’s long ranged weapons.

 

It seemed as though they were evenly matched, as they fought against each other relentlessly. When the time was right, 9S took the chance to charge at A2 in an attempt to stab her. However… a loud scream of agony could be heard as A2 plunged her sword into his stomach, while he did the same to her.  
“ **Nines** **!** ” 13S quickly ran towards him as he laid there writhing in agony, trying to remove it.  
She was panicking now. Was removing the blade truly a good idea? It had been lodged far enough into him for it go right through his back.  
“ **N** **o!** No no, no, no, no, no, no, Nines!” She whimpered, moving to his side.  
“Nines, hold on!” She cried, trying to access the damage.  
“Pod, you have to help me repair him!”  
“I do not believe that is an available option. The possibility of successful repair is of 0 percent probability, given his current status.”  
“ **We have to try** **!** ” She yelled, watching as the life slowly began to drain from his face.  
“Please, **please** … hold on for just a little longer.” She begged.  
9S tried his best to speak, the sound that came from his throat was strained and weak.  
“ **Stop trying to talk** **!** Y **ou have to conserve your energy!** ” She told him.  
“I… I’m going to remove the sword a-and... try to repair you, so just… just bear with me, okay!?”

Before she could try however, 9S weakly took her hand.  
“Thir...teen. I’m...sor...ry.” He croaked, holding her hand tightly.  
“ **I told you to stop talking!** ”  
“I… c-couldn’t… .k-eep… my promise… to you.”  
13S sniffled and shook her head as she took his hand.  
“T-that’s not true. You can still keep it. I just… have to remove the sword and wrap up your wound and then… we can get you repaired at the resistance camp or something. I… I’m sure that Pascal will have… the parts to help us?” She said, as tears began to stream down her cheeks.

9S weakly shook his head and slowly reached up, placing his hand on her cheek, his eyes half-lidded and still glowing red.  
“I can’t… s-stay… aw-awake… for that...long.” 9S whispered.  
“S-sorry...”

 

The tears running down her cheeks had landed upon his face, as she reached up and placed her hand on top of his.  
“D-don’t be s-sorry. I’m sure… I’m s-sure there’s a way to fix this. What if I just…?” 13S’s voice began to crack.  
“If you could… just...” The young android didn’t get a chance to finish her sentence, as 9S’s hand fell away from her face and the color in his eyes began to dull, as they completely closed.  
13S’s cries turned into heartbroken sobs as she held his body close to her, cradling his head as she screamed at the top of her lungs.  
Her mournful sobs continued to grow louder, and louder as she began to rock back and forth, holding her lover’s cold, lifeless body while calling out his name and begging him to wake up.  


“There is a way to fix this.” A familiar voice, said as the girls in red suddenly appeared before her.  
“W-what do you mean?”  
“We can bring him back for you, but at a price.” They answered.  
“What do I have to do?” She asked, gently running her fingers through his hair.  
“In order to save him, you will have to start over from the beginning at the price of losing your current memories.” They explained.

“However, you only have a limited time to decide. He will soon fade away and we won’t be able to bring him back.” They informed her.  
“What is your answer?”  
“I’ll do it.” She whispered, looking up at them.  
“I want to fix this. I want to bring Nines back.” She replied.

Quickly the girls shoot towards her, one entering her body as the other seemed to enter 9S.  
With a sudden burst of light, 13S found herself in hack-space in her own body.  
_“Tell me what I have to do.”_ She ordered, her eyes taking in her surroundings.  
_“You must find Adam and Eve, and_ _tell_ _them_ _that you wish_ _to_ _start over_ _.”_ They explained. __  
“ _W_ _e shall give you a hint since your attraction to_ _him_ _amuses us and we find it worthy of study.”_ They added.  
_“Continue on the path until you find the door that will lead you to salvation.”_

 _“The door to salvation?”_  
“I believe that could symbolize the heart or the mind.” Pod 148 responded.  
13S looked around as she tried to figure out which direction she could take to get there as fast as possible.  
  
The further in she got, the sound of a conversation could be heard all around her.  
“My name...is 9S. I am a YoRHa type Scanner model. I was created on...”  
_“Wait, do you hear that?”_  
“Affirmative. It sounds like the voice of 9S. I speculate that he is going through his memories.”  
“Which direction is it coming from?”  
“Unknown.”

 _“If he truly is recovering his memories, wouldn’t that mean it’s coming from his brain?”_ 13S asked. _  
“The fastest possible route to the brain, is straight ahead.”_ The pod replied, as 13S continued down the path.

 

It took a long time for 13S to finally reach the room where she believed the so called ‘door to salvation’ was located.  
When she got there, she didn’t expect there to be two doors.  
_“Oh no, which door is it?”_ She asked, staying quiet as she listened for his voice.  
“Adam and Eve are in the ark. Eve is asleep. Adam holds...”  
_“There!”_ She exclaimed, quickly running through the door on the right.  
_“Nines!”_ She called, standing in the middle of the room and looking around.  
The space around them actually looked like...a replica of the Bunker.  
In the middle of the room stood a visage of 9S, along with the images of both Adam and Eve, with Adam’s hand outstretched.  
“Will you come with us?” She heard Adam ask as he gazed at 9S.  
_**“NO!”**_ She yelled, rushing towards them and standing in front of 9S with her arms outstretched. “Thirteen? How did you… get here?”  
_**“I WON’T LET YOU TAKE HIM FROM ME! NOT AGAIN!”**_ She cried, staring at them as Eve began to stir.  
This act alone had caught them off guard.  
“Who… is this?” asked Adam, as Eve watched her tiredly.  
_“My name is 13S and I’ve come to start over!”_ She replied.  
“Start over?”  
13S nodded. _“I want to start over and… save 9S!”_

“You what?” Eve asked, sitting up now.  
_“I want to save 9S and bring him back. He doesn’t deserve to die.”_ She told them. _  
“So please, let me start over for him.”_

The room was silent as Adam and Eve looked at each other, then shifted their gaze to 13S, who was still standing in front of 9S.  


“Wait Thirteen, what do you mean by start over and what happens when you do?” 9S asked, still standing behind her.  
“What the girl means is that, she wants to give up her life for yours. Isn’t that right, 13S was it?”  
_“Yes.”_  
“What? No!” 9S exclaimed as he stood in front of her now.  
“Thirteen, you can’t just give up your life for me!”  
“ _Why not? You gave up yours for 2B, didn’t you?”_ She asked, looking away from him with her arms at her side.  
9S was taken aback as he stared at her. “I… it’s not… like that Thirteen.”  
_“Oh yeah? Then what was it like? It seemed to me that you cared more about 2B than you did for me.”_ She replied.  
_“Was everything you told me a lie?”_  
“No! I was upset about 2B’s murder and I promise that everything I told you was true.” He reassured.  
_“Please, remember for me and know that no matter what… I will always love you 9S.”_ She said, kissing him softly before walking over to Adam and Eve.  
“Do you still wish to start over?” asked Adam, as Eve made his way towards 9S and stood behind him, placing his hands on his shoulder.

_“Yes, please let me start over.”_

“Very well, then answer me this one question...” Adam said, reaching out for her.  
“Will you come with us?”  
13S looked back at 9S, before returning her gaze to Adam and nodding.  
_“Of course, I’ll go with you.”_ She replied, taking his hand.

 

After taking his hand, a bright light engulfed them and 13S found herself floating in a vast expanse of nothing but white light.  
It seemed as if she would float there forever, until she landed on what appeared to be solid ground in a place that seemed all too familiar.  
“Is this… hack-space?” She asked, looking around.  
_“How long has she been out?”_ A voice asked, cutting through the silence.  
_“For about two weeks now.”_ Another voice replied.  
“Two weeks?” 13S replied, looking around.  
Where were the voices coming from?  
_“Are we still not allowed to hack her?”_  
“No, the Commander suggested that we wait for her to wake up. Hacking her will only cause more harm than good.” The second voice responded.  
“They’re waiting… for me to wake up?”  
_“Has Nines been with her this entire time?”_ A male voice asked.  
_“Yes, he’s been trying his best to wake her up”_ The other female voice answered.  
_“Thirteen… I know you can hear me.”_ Came a second male’s voice.  
_“Please follow my voice, and come back to us. Come back to me.”_ The voice begged.  
_“It’s not the same without you here. I miss your smile and your laughter.”_ He said.  
_“I miss… everything about you. So please, come back.”_  
13S ran as fast she could, sprinting down the continuously winding path.  
Who did those voices belong to and how did they know her?  
Most importantly, who was the one that said he missed her?

 

The path to the source of the voices seemed like a long and arduous journey. Reaching a room with two doors, 13S entered the door on the left.  
“Has she still not woken up yet?” 21O asked, leaning against the wall of the building.  
“Not yet.” 2B answered, sighing heavily as she leaned against the wall as well.  
“Do you think she ever will? She **has** been out for two weeks already. Maybe we should give up on her.”  
“No, we can’t. She’ll wake up soon, I know she will.” 9S replied, his voice sounded tired as he held her hand tight while gazing at her.  
“Wasn’t she heavily damaged by the EMP waves? Do you think she’ll even remember us if she does, wake up?” 21O wondered, gazing at 13S’s sleeping form.  
“If she doesn’t, we'll be here to help her remember.” 56B replied.

At that moment, 13S began to stir as her eyes slowly began to open.  



End file.
